PLUMED-NEST

Project ID: plumID:23.044
Source: plumed_files/plumed.dat
Originally used with PLUMED version: 2.5
Stable: zipped raw stdout - zipped raw stderr - stderr
Master: zipped raw stdout - zipped raw stderr - stderr

Click on the labels of the actions for more information on what each action computes

fullThe GROUP action with label full calculates the following quantities:
 Quantity   
 Type   
 Description  
full
atoms
indices of atoms specified in GROUP: 
GROUP
Define a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details
 
ATOMS
the numerical indexes for the set of atoms in the group
=1-60
cppThe GROUP action with label cpp calculates the following quantities:
 Quantity   
 Type   
 Description  
cpp
atoms
indices of atoms specified in GROUP: 
GROUP
Define a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details
 
ATOMS
the numerical indexes for the set of atoms in the group
=198-297
c1The COORDINATION action with label c1 calculates the following quantities:
 Quantity   
 Type   
 Description  
c1
scalar
the value of the coordination: 
COORDINATION
Calculate coordination numbers. This action has hidden defaults. More details
 
GROUPA
First list of atoms
=full 
GROUPB
Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
=cpp 
R_0
The r_0 parameter of the switching function
=0.25 
c1: 
COORDINATION
Calculate coordination numbers. This action uses the defaults shown here. More details
 
GROUPA
First list of atoms
=full 
GROUPB
Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
=cpp 
R_0
The r_0 parameter of the switching function
=0.25  
D_0
 The d_0 parameter of the switching function
=0.0 
NN
 The n parameter of the switching function 
=6 
MM
 The m parameter of the switching function; 0 implies 2*NN
=0
METAD
Used to performed metadynamics on one or more collective variables. More details
 ...
 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=metadThe METAD action with label metad calculates the following quantities:
 Quantity   
 Type   
 Description  
metad.bias
scalar
the instantaneous value of the bias potential
metad.acc
scalar
the metadynamics acceleration factor
 
ARG
the input for this action is the scalar output from one or more other actions
=c1
 
HEIGHT
the heights of the Gaussian hills
=2
 
PACE
the frequency for hill addition
=20000
 
SIGMA
the widths of the Gaussian hills
=0.5
 
BIASFACTOR
use well tempered metadynamics and use this bias factor
=20
 
GRID_MIN
the lower bounds for the grid
=0
 
GRID_MAX
the upper bounds for the grid
=100
 
GRID_BIN
the number of bins for the grid
=400
 
FILE
 a file in which the list of added hills is stored
=HILLS
 
ACCELERATION
 Set to TRUE if you want to compute the metadynamics acceleration factor
... METAD

COMMITTOR
Does a committor analysis. More details
 ...
  
ARG
the input for this action is the scalar output from one or more other actions
=c1
  
STRIDE
 the frequency with which the CVs are analyzed
=500
  
BASIN_LL1
List of lower limits for basin #
=-0.1
  
BASIN_UL1
List of upper limits for basin #
=0.1
... COMMITTOR

The COMMITTOR action with label  calculates something
PRINT
Print quantities to a file. More details
 
ARG
the input for this action is the scalar output from one or more other actions
=c1,metad 
FILE
the name of the file on which to output these quantities
=COLVAR 
STRIDE
 the frequency with which the quantities of interest should be output
=500